Synthetic Biology Engineering Research Center

Synberc Blog

  • Kevin Costa |

    There seems to be a lot of commotion in the synthetic biology community these days about how to organize our research community at the national level. This is definitely true within Synberc, where our Sustainability Project has been critically assessing what is needed to responsibly advance the field.

    For all of the hullabaloo, there’s very little actual organizing going on at the national level. The field has defaulted into a “communities of practice” mode, where smaller groups of practitioners of a particular interest or expertise naturally come together to share information and experience, and have an opportunity to develop themselves personally and professionally, or to advance a particular agenda.

    Here are some specific examples of how the synthetic biology community has self-organized:

    • iGEM - The “world’s premiere synbio competition” but also an important testbed for educating synthetic biologists, creating a shared database of parts, and for learning how to screen projects for safety/security concerns. Probably the most successful effort to organize the synbio community not just in the US but worldwide.
    • SynBioBeta - A recent but highly successful effort led by one organizing dynamo (John Cumbers, Santa Clara University/NASA Ames) that is bringing together small start-up companies and other entrepreneurially minded interests to foster the “synthetic biology start-up ecosystem.”
    • BioBricks Foundation - An early pioneer in trying to bring together the synthetic biology community in more or less the mode of a professional society. BBF runs the SBX.0 International Conference Series, which is the synbio community’s primary conference. BBF has also led a call for technical comments that led to the development of a BioBricks Public Agreement (BPA) to enable easier sharing of biological parts.
    • The DIYbio 'movement' is a good example of how citizen scientists and enthusiasts are organizing themselves at the very local levels -- the DIYbio community has not yet developed a strong guild at the national level, but the potential appears to be there.
    • Synberc - The US’s first and largest single effort to bring together leading researchers and universities to establish the scientific and engineering foundations of synthetic biology. It too was generated at the grassroots level by a group of like-minded researchers, rather than by a national fiat.

    One more important way in which the community is organizing itself: A crop of synthetic biology centers has blossomed at individual universities:

    The formation of these centers suggest that the community is hungry for organizational entities that last over many years and help researchers from diverse backgrounds come together to pursue shared research aims.

    Zooming back out to the national level, the basis set of leaders in synthetic biology are often recombined in different ways to address different problems in different contexts. For example, many of the experts involved in a NAS study on technical roadmaps are likely to be seen at another study on the ethical, legal and social ramifications of synthetic biology. The basis set of leaders is slowing growing outward as the field identifies new opportunities/challenges and becomes aware of and comfortable with others from different research communities. As with any highly multidisciplinary endeavor, the challenge for our community is to enable and encourage diverse practitioners with shared goals to come together to solve problems we cannot solve independently.

    In the UK, the scientific community has had better success in organizing itself at the national level, especially through the UK Roadmap process. One might argue about the practical value of the technology and society roadmap that such efforts produce, but the roadmap itself is probably not as important as bringing together new assemblages of scientists, policymakers, funders, and other stakeholders to think about the opportunities and challenges of synthetic biology from many perspectives. The report accompanying the roadmap has a number of important insights (IMHO) and did seem to result in the national synergy in synbio that the UK is now experiencing.

    Given the current status of organizing in the US and the need to develop a more coordinated framework, one might consider something like a spoke-and-hub model for getting there. In a sense, this is what Synberc is. The universities are bound together loosely by Synberc. The colleges and their investigators are free to pursue independent projects and even engage in cooperative competition, yet they can leverage Synberc infrastructure for thinking about "problems of the commons". These include strategic roadmapping, responsible innovation, education and workforce development, industry liaison (e.g., creating a one-stop shop for industry members to interact with leaders of the field), addressing intellectual property concerns, metrology and standards, communications & advocacy (enabling the community to speak with a common voice), and simply building community through regular symposia and workshops. Given the proliferation of “communities of practice” across the U.S. in synthetic biology, an elastic organization may be the only kind that can accommodate such a wide range of researchers and organizations.

  • Linda Kahl |

    Linda KahlOn July 13, 2013 the U.S. Supreme Court issued their decision in Association for Molecular Pathology v. Myriad Genetics, Inc. Naturally, this decision has sparked much discussion amongst the synthetic biology research community. What does this decision mean with regard to the patentability of synthetic constructs created from natural DNA sequences? Does this decision mean that the information contained within DNA sequences is patentable? And, ultimately, how will this decision affect innovation in synthetic biology?

    It is important to keep in mind that the court limited their decision to only one inquiry under U.S. patent law: Does isolated DNA or cDNA constitute patentable subject matter under 35 USC 101? The short answer is: NO for isolated DNA based on natural sequences, and MAYBE for cDNA molecules - see end of first paragraph, page 17.

    The court specifically expressed no opinion whether cDNA satisfies the other requirements for patentability such as novelty (35 USC 102), non-obviousness (35 USC 103), and enablement/definiteness (35 USC 112) - see footnote 9.

    As is typical of U.S. Supreme Court decisions, the full impact will be become more apparent as the lower courts interpret this decision in subsequent cases. While we may not yet have answers to all of our questions, we do have more certainty today than we did before.

    What we know for sure is that this decision renders invalid any claim with the structure “isolated DNA having SEQ ID NO: 1”

  • Christina Agapakis |

    ChristinaSynthetic biology is often referred to as "the field of the future," the foundation of a "third industrial revolution" that will change the way we produce fuelsmaterialsmedicines, as well as the way we produce knowledge of biological systems. But while the self-consciously revolutionary language of synthetic biology declares a change of the industrial status quo, the metaphors we rely on are explicit references to the successful revolutions of past industrial technologies.

    The term synthetic biology echoes the successes of synthetic chemistry, while the guiding concept of standardization in genetic components is modeled on 19th century standardization of interchangeable parts. Industrial metaphors mix further as we climb the abstraction hierarchy; genetic parts are assembled to fit into a cellular chassis, creating logic gates and circuits that can compute biological information, leading to the control of cellular factories.

    der menschThese metaphors help us to understand how an industrial revolution might emerge from a biology lab, showing a possible path from ideas to industry. Like the "horseless carriage," perhaps the analogies of living cells to computers give us a sense of familiarity with a technology whose potential we have not yet fully grasped. Industrial metaphors have long played a role in how we understand biology and the human body, from Fritz Kahn’s 1927 paintings of “Man as Industrial Palace” to  analogies between brains and computers. By referencing the products and methods of previous industrial revolutions, synthetic biology aims not only to aid understanding but also to demonstrate the future potential of the field. These metaphors draw the projected lines of Moore's exponential increase as strands of DNA, imagining analogous and expanding industries based on carbon and sunlight rather than silicon and fossil fuels. 

    Kuhn SSRHow will this revolutionary transition happen? What conditions are necessary to foster such a change? As synthetic biology is largely still a laboratory rather than industrial enterprise, perhaps Thomas Kuhn's The Structure of Scientific Revolutions, can provide a useful framework for understanding the structure of the promised techno-scientific-industrial revolution of synthetic biology. Based on his analysis of the history of chemistry and physics, Kuhn argues that the evolution of scientific knowledge proceeds by punctuated equilibrium — periods of "normal science" interrupted by scientific revolutions, paradigm shifts that change the nature of the questions being asked and the "puzzles" being solved. Paradigms shift after the accumulated weight of unexpected results becomes too large, when facts that don’t fit the model begin to open new questions and when the "failure of existing rules is the prelude to a search for new ones."

    Some of the failures of modern industry are explicit starting points for synthetic biology projects, like engineered bacteria that can sense or consume industrial pollutants, but norevolution can address all the failures of the paradigms that came before. For scientific revolutions, Kuhn writes, "To be accepted as paradigm, a theory must seem better than its competitors, but it need not, and in fact never does, explain all the facts with which it can be confronted." What problems can synthetic biology solve and what problems are missed, outside of the paradigmatic umbrella of biotechnology? What new problems might arise with a biology-based industrial revolution?

    These are difficult and important questions with no clear answer, questions that we ask ourselves when we talk about risk, implications, and outcomes of new technologies. But perhaps there is a deeper question that emerges when we look at synthetic biology through a Kuhnian lens: by working to solve the problems of current industry, replacing or cleaning up after polluting chemical factories with microscopic cellular factories, are we simply replicating the old paradigm with a biological tint? Are we talking revolution while just solving puzzles?

    Industrial metaphors for biological systems are being inverted, but the industrial paradigm remains: “Man as Industrial Palace” becomes “Industrial Palace in a Cell.” How can a biologically driven industry change these metaphors, change the way we make things and the way we do things that takes biology on its own terms, that changes the paradigm through which we see the world?

    Within synthetic biology, programs that I’ve been involved with such as Synthetic Aesthetics and the Synthetic Biology Leadership Excellence Accelerator Program (LEAP)--sponsored by Synberc's Practices thrust--are efforts to integrate new questions, metaphors, and paradigms into the research goals and visions of synthetic biologists. Synthetic Aesthetics joins artists and designers with scientists and engineers to consider not just implications of the products of synthetic biology but to reconsider what those products might be—the metaphors that we use to understand and design nature. LEAP has different but complementary goals, bringing together scientists and engineers in academia and industry with experts from policy, ethics, economics, and law and providing a space to creatively consider what it would mean for synthetic biology to work in the public interest.

    Both programs encourage those involved with synthetic biology to think beyond existing paradigms, both in science and industry. Conversations like these may help us to push beyond the industrial metaphors that we depend on when we talk about the potential of synthetic biology, providing us with new paradigms that can be truly revolutionary.

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    Tune into Christina's regular blog at Scientific American. 

  • Linda Kahl |

    It’s a particularly exciting time for synthetic biology and for developments in intellectual property law.  Advances in the engineering of biology are deepening our understanding of how biological systems work and leading to new applications that could help promote human health and preserve the environment.  At the same time, tremendous advances in patent law are changing the way in which innovators seek protection for their intellectual property rights.

    The sweeping reforms to U.S. patent law brought about by the Leahy-Smith America Invents Act have created new opportunities and challenges for the synthetic biology research community.  On March 16th of this year the U.S. transitioned to a “first-inventor-to-file” priority system for patents, which is more aligned with the patent laws of other countries and will impact the strategic choices made by synthetic biology researchers seeking patent protection for their inventions.  

    Other exciting changes to U.S. patent law include crowdsourcing the examination of patent applications as well as broadening public participation in the post-grant review of issued patents.  These changes open up new possibilities for the synthetic biology research community to engage with the U.S. patent system and help ensure that patent protection is awarded only for inventions that truly merit a 20-year grant of monopoly rights.

    Court decisions affecting the interpretation of patent laws also may impact innovation in synthetic biology.  One case currently before the U.S. Supreme Court – Association for Molecular Pathology v. Myriad Genetics, Inc. – addresses the patentability of isolated DNA and cDNA molecules. While the Myriad case specifically focuses on DNA derived from human genes, the decision could shed light on the patentability of synthetic DNA derived from natural sources.  Oral arguments for the Myriad case are scheduled to take place on April 15th.

    Another case currently before the U.S. Supreme Court – Bowman v. Monsanto, Inc. – examines whether patent holders can enforce their patent rights on the products of self-replicating technologies after an authorized sale. The Bowman case is specifically looking at seeds from genetically modified plants, but self-replicating technologies abound in synthetic biology and the decision could impact the commercial development of useful products and constructive applications of synthetic biology. Oral arguments for the Bowman case were held on February 19th and a decision is expected by June.

    Here at Synberc, we are focusing on how property rights can best be applied and adapted to promote innovation in synthetic biology. We’re conducting a survey of the enabling technologies of synthetic biology so that we and others can systematically investigate the property rights associated with these technologies. We’re also developing a portfolio of options that will explore possible legislative changes as well as policy initiatives and community actions to more effectively work within the existing patent-based legal framework. We anticipate these options will not present a complete solution for all the property rights issues encountered in the emerging field of synthetic biology, but instead will serve to inform and contribute to broader discussions about the optimal use of property rights to promote innovation in synthetic biology and biotechnology, more generally.

    Linda Kahl, Ph.D., J.D.
    Legal Scholar, Synberc

  • Jay Keasling |

    Hello and welcome to our blog! Here you'll find informative opinion pieces about a range of issues in the field of synthetic biolgy, researcher profiles, and helpful resources in the form of both videos and text. Please join us here each week for commentary created by and for members of our community.

    Stay tuned for Linda Kahl's blog next week, where she discusses U.S. patent law reform and current U.S. Supreme Court cases that may impact the ways in which DNA might be patented, as well as whether patent holders can enforce their patent rights on the products of self-replicating technologies after an authorized sale.

    Also on deck is a blog from Christina Agapakis on the impact of Synberc's Leadership Excellence Accelerator Program.

    If you'd like to contribute a posting, please contact Kevin Costa (kcosta@berkeley.edu) for submission guidelines. We're looking forward to hearing from all of the voices in our community!

    Jay Keasling
    Director, Synberc